Re: [R] Question on output of vectors from a for loop into a matrix

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California

Re: [R] ROC curve in R

On Thursday 26 July 2007 10:45, Frank E Harrell Jr wrote: Dylan Beaudette wrote: On Thursday 26 July 2007 06:01, Frank E Harrell Jr wrote: Note that even though the ROC curve as a whole is an interesting 'statistic' (its area is a linear translation of the Wilcoxon-Mann-Whitney-Somers

Re: [R] ROC curve in R

On Thursday 26 July 2007 06:01, Frank E Harrell Jr wrote: Note that even though the ROC curve as a whole is an interesting 'statistic' (its area is a linear translation of the Wilcoxon-Mann-Whitney-Somers-Goodman-Kruskal rank correlation statistics), each individual point on it is an improper

[R] reversing the x-axis terms on a boxplot

Hi, I am able to reverse the order of plotting on regular plots (i.e. with the plot() function) by manually setting the xlim variable. Is there some trick like this which will work for a boxplot? * for example: l - sample(letters, 500, replace=TRUE) n - runif(500) boxplot(n ~ l) this will

[R] DF and intercept term meaning for mixed (lme) models

Hi, I am using the lme package to fit mixed effects models to a set of data. I am having a difficult time understanding the *meaning* of the numDF (degrees of freedom in the numerator), denDF (DF in the denomenator), as well as the Intercept term in the output. For example: I have a

Re: [R] inter-rater agreement index kappa

, method='kendall') cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] off-topic: affine transformation matrix

, 28 May 2007, Dylan Beaudette wrote: This may sound like a very naive question, but... give two lists of coordinate pairs (x,y - Cartesian space) is there any simple way to compute the affine transformation matrix in R. I have a set of data which is offset from where i know it should be. I

[R] off-topic: affine transformation matrix

, and matching coordinates of where the data should be. I need to compute the composition of the affine transformation matrix, so that I can apply an affine transform the entire dataset. any ideas? thanks in advance! -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University

Re: [R] aggregate similar to SPSS

@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dylan Beaudette Soil Resource Laboratory http

[R] locate nearest value in lookup table

Hi everyone, I have a pile of data derived from an analytical device, which reports values as a continuous distribution. I need to associate classes (based on the Munsell color system) using a standard look-up table - the problem is that I would like to find the *closest* matching entry in the

Re: [R] prop.test or chisq.test ..?

On Wednesday 28 February 2007 01:07, Christoph Buser wrote: Hi Some comments are inside. Dylan Beaudette writes: Hi everyone, Suppose I have a count the occurrences of positive results, and the total number of occurrences: pos - 14 total - 15 testing

[R] prop.test or chisq.test ..?

intuition, but affirmation would be great. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] model diagnostics for logistic regression

, is there any facility to calculate the R^{2)_{L} as suggested by Menard in Applied Logistic Regression Analysis (2002) ? Any thought would be greatly appreciated. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

[R] sample size calculations

, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

[R] extra panel arguments to plot.nmGroupedData {nlme}

Greetings, I have a groupedData (nmGroupedData) object created with the following syntax: Soil - groupedData( ksat ~ conc | soil_id/sar/rep, data=soil.data, labels=list(x='Solution Concentration', y='Saturated Hydraulic Conductivity'), units=list(x='(cmol_c)', y='(cm/s)') ) the

Re: [R] memory problem [cluster]

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dylan Beaudette Soils

[R] evaluation of 2 matrices: categorical comparison

to get. Thanks in advance, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] any good way to convert sp class objects to splancs object

Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

Re: [R] any good way to convert sp class objects to splancs object

On Wednesday 25 October 2006 12:02, Roger Bivand wrote: On Wed, 25 Oct 2006, Dylan Beaudette wrote: Greetings: are there any simple ways to convert an sp class object to a splancs ppp class object, outside of reading the coordinates and computing a bounding box? Aren't ppp class

Re: [R] compiling rgdal package on windows / macos

On Thursday 05 October 2006 02:06, Roger Bivand wrote: On Wed, 4 Oct 2006, Dylan Beaudette wrote: Greetings: As I am not a windows user, I cannot try this: is it possible to install rgdal on windows without having to compile it from source ? Andy Jaworski already replied that rgdal

[R] compiling rgdal package on windows / macos

-config --- which was recently installed with GRASS. I have updated my PATH environment variable, logged out, but R still cannot find the gdal-config program. any tips on getting the rgdal package up and running on MacOS or Windows would be greatly appreciated. Cheers, -- Dylan Beaudette Soils

[R] mysterious error on compile R 2.3.1

]: Leaving directory `/home/dylan/src/R-2.3.1/src/library/Recommended' make: *** [stamp-recommended] Error 2 note that i am using the GCC flags: CFLAGS=-march=opteron -ffast-math CXXFLAGS=-march=opteron -ffast-math any ideas? -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University

Re: [R] mysterious error on compile R 2.3.1

On Wednesday 20 September 2006 12:38, Peter Dalgaard wrote: Dylan Beaudette [EMAIL PROTECTED] writes: Getting a very strange error with a new install of R from source on x86; make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src' ** R ** data ** moving datasets to lazyload DB

Re: [R] questions regarding spline functions

] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dylan Beaudette Sent: Monday, July 31, 2006 6:43 PM To: RHELP Subject: [R] questions regarding spline functions Greetings, A couple general questions regarding the use of splines to interpolate

[R] questions regarding spline functions

sample code Any thoughts / input would be greatly appreciated! Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 spline1.png Description: PNG image __ R-help@stat.math.ethz.ch mailing

Re: [R] how to use large data set ?

]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dylan Beaudette Soils and Biogeochemistry Graduate

Re: [R] coloring leaves in a hclust or dendrogram plot [solved]

of the dendrogram are truncated. Is there any way to prevent this - some parameter that I can pass to A2Rplot() ? Also, is it possible to add more factors to the bottom of the plot? Thanks! Dylan -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis

[R] standardization of values before call to pam() or clara()

if this is statistically correct. Any ideas, thoughts would be greatly appreciated. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https

Re: [R] passing known medoids to clara() in the cluster package

Martin, Just wanted to check on the status of including known medoids into calls to the clara() function within the cluster package. Cheers, Dylan On Monday 10 April 2006 14:25, Dylan Beaudette wrote: Thanks for the reply. On Sunday 09 April 2006 11:46 pm, Martin Maechler wrote: DylanB

Re: [R] passing known medoids to clara() in the cluster package

Thanks for the reply. On Sunday 09 April 2006 11:46 pm, Martin Maechler wrote: DylanB == Dylan Beaudette [EMAIL PROTECTED] on Sun, 9 Apr 2006 19:28:44 -0700 writes: DylanB Greetings, I have had good success using the clara() DylanB function to perform a simple cluster analysis

[R] passing known medoids to clara() in the cluster package

clara() know about the classes that I have in mind. Is this at all feasible, or am I trying to accomplish something that is not possible? Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

Re: [R] transform shapefiles in UTM to lat/long

performing the inverse projection with the GDAL/OGR library first. -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] coloring leaves in a hclust or dendrogram plot [solved]

On Thursday 09 March 2006 06:12 pm, Dylan Beaudette wrote: Greetings, I have perused the r-help mailing list archives for an answer to this question, without avail. I would like to color the leaves of a dendrogram plot based on a cutoff in one of the variables involved in the initial

[R] coloring leaves in a hclust or dendrogram plot

, ] Such that leaves in the tree will be colored based on the membership in either of the two above groups. Is there a resource documenting how this might be accomplished? Any thoughts or ideas would be greatly appreciated. Cheers, Dylan -- Dylan Beaudette Soils and Biogeochemistry Graduate Group

[R] extracting RGB values from a colorspace class object

is an example of the output: http://169.237.35.250/~dylan/temp/soil_colors-LUV_space.png Somehow the plot() method in the colorspace package is converting color space coordinates to their RGB values... Does anyone have an idea as to how to access these RGB triplets? Thanks in advance! -- Dylan

Re: [R] understanding patterns in categorical vs. continuous data

, fun = summary) On 1/26/06, Dylan Beaudette [EMAIL PROTECTED] wrote: Greetings, I have a set of bivariate data: one variable (vegetation type) which is categorical, and one (computed annual insolation) which is continuous. Plotting veg_type ~ insolation produces a nice overview

[R] understanding patterns in categorical vs. continuous data

, or suggested reading material would be greatly appreciated. -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r

[R] overlay additional axes

(TIK[,1]/2*pi/180)) ? thanks in advance! -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] finding peaks in a simple dataset with R

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Wow! This was the exact sort of simple peak finding algorithm I was looking for. Would it be ok for me to post this to our dept. webpage so that others may use it? Cheers, -- Dylan

Re: [R] finding peaks in a simple dataset with R

(peaks(y,7), col=3) Thanks for working on this, as I would imagine there are other lurkers out there who are waiting for a solution to this problem. -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341

Re: [R] finding peaks in a simple dataset with R

the analysis: getPeaks(X,peakfile) #errors with: Error in area/max(area) : non-numeric argument to binary operator In addition: Warning message: no finite arguments to max; returning -Inf any ideas would be greatly appreciated! -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University